Statistical Applications in Genetics and Molecular Biology

2002 - 2024

Current editor(s): Michael P. H. Stumpf

From De Gruyter
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Volume 18, issue 6, 2019

A Bayesian framework for identifying consistent patterns of microbial abundance between body sites pp. 15

Meier Richard, Thompson Jeffrey A., Chung Mei, Zhao Naisi, Kelsey Karl T., Michaud Dominique S. and Koestler Devin C.

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics pp. 20

Crook Oliver M., Gatto Laurent and Kirk Paul D. W.

EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples pp. 23

Madsen Tobias, Świtnicki Michał, Juul Malene and Pedersen Jakob Skou

Determining the number of components in PLS regression on incomplete data set pp. 28

Nengsih Titin Agustin, Bertrand Frédéric, Maumy-Bertrand Myriam and Meyer Nicolas

Volume 18, issue 5, 2019

A novel individualized drug repositioning approach for predicting personalized candidate drugs for type 1 diabetes mellitus pp. 9

Zheng Hong

Bi-level feature selection in high dimensional AFT models with applications to a genomic study pp. 11

Huang Hailin, Shangguan Jizi, Ruan Peifeng and Liang Hua

Stability selection for lasso, ridge and elastic net implemented with AFT models pp. 14

Khan Md Hasinur Rahaman, Bhadra Anamika and Howlader Tamanna

Clustering methods for single-cell RNA-sequencing expression data: performance evaluation with varying sample sizes and cell compositions pp. 14

Suner Aslı

Volume 18, issue 4, 2019

A penalized regression approach for DNA copy number study using the sequencing data pp. 14

Lee Jaeeun and Chen Jie

Inference of finite mixture models and the effect of binning pp. 20

Geissen Eva-Maria, Hasenauer Jan and Radde Nicole E.

Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data pp. 25

Lim Johan, Yu Donghyeon, Kuo Hsun-chih, Choi Hyungwon and Walmsley Scott

Properties and Evaluation of the MOBIT – a novel Linkage-based Test Statistic and Quantification Method for Imprinting pp. 40

Brugger Markus, Knapp Michael and Strauch Konstantin

Volume 18, issue 3, 2019

Reproducibility of biomarker identifications from mass spectrometry proteomic data in cancer studies pp. 13

Liang Yulan, Kelemen Adam and Kelemen Arpad

Combining gene expression data and prior knowledge for inferring gene regulatory networks via Bayesian networks using structural restrictions pp. 14

M. de Campos Luis, Cano Andrés, Castellano Javier G. and Moral Serafín

Data-adaptive multi-locus association testing in subjects with arbitrary genealogical relationships pp. 15

Gong Gail, Wang Wei, Hsieh Chih-Lin, J. Van Den Berg David, Haiman Christopher, Oakley-Girvan Ingrid and Whittemore Alice S.

netprioR: a probabilistic model for integrative hit prioritisation of genetic screens pp. 16

Schmich Fabian, Kuipers Jack, Merdes Gunter and Beerenwinkel Niko

Volume 18, issue 2, 2019

LCox: a tool for selecting genes related to survival outcomes using longitudinal gene expression data pp. 9

Sun Jiehuan, Herazo-Maya Jose D., Wang Jane-Ling, Kaminski Naftali and Zhao Hongyu

A powerful test for ordinal trait genetic association analysis pp. 9

Xue Yuan, Wang Jinjuan, Ding Juan, Zhang Sanguo and Li Qizhai

Discrete Wavelet Packet Transform Based Discriminant Analysis for Whole Genome Sequences pp. 12

Huang Hsin-Hsiung and Girimurugan Senthil Balaji

A multivariate linear model for investigating the association between gene-module co-expression and a continuous covariate pp. 13

Padayachee Trishanta, Khamiakova Tatsiana, Shkedy Ziv, Salo Perttu, Perola Markus and Burzykowski Tomasz

Volume 18, issue 1, 2019

MLML2R: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions pp. 6

Kiihl Samara F., Martinez-Garrido Maria Jose, Domingo-Relloso Arce, Bermudez Jose and Tellez-Plaza Maria

Meta-analytic framework for modeling genetic coexpression dynamics pp. 13

Kinzy Tyler G., Starr Timothy K., Tseng George C. and Ho Yen-Yi

Sliced inverse regression for integrative multi-omics data analysis pp. 13

Jain Yashita, Ding Shanshan and Qiu Jing

Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model pp. 17

Li Xiaohong, Wu Dongfeng, Cooper Nigel G.F. and Rai Shesh N.

Volume 17, issue 6, 2018

False discovery control for penalized variable selections with high-dimensional covariates pp. 11

He Kevin, Zhou Xiang, Jiang Hui, Wen Xiaoquan and Li Yi

A practical approach to adjusting for population stratification in genome-wide association studies: principal components and propensity scores (PCAPS) pp. 12

Zhao Huaqing, Mitra Nandita, Kanetsky Peter A., Nathanson Katherine L. and Rebbeck Timothy R.

A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series pp. 14

Zhang Fang, Shan Ang and Luan Yihui

Volume 17, issue 5, 2018

Assessing genome-wide significance for the detection of differentially methylated regions pp. 8

Page Christian M., Vos Linda, Rounge Trine B., Harbo Hanne F. and Andreassen Bettina K.

A test for detecting differential indirect trans effects between two groups of samples pp. 11

Chaturvedi Nimisha, Menezes Renée X. de, Goeman Jelle J. and Wieringen Wessel van

A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data pp. 14

Perrot-Dockès Marie, Lévy-Leduc Céline, Chiquet Julien, Sansonnet Laure, Brégère Margaux, Étienne Marie-Pierre, Robin Stéphane and Genta-Jouve Grégory

Volume 17, issue 4, 2018

Editorial change at Statistical Applications in Genetics and Molecular Biology pp. 1

Krüger Torsten

Biology challenging statistics pp. 2

Stumpf Michael P.H.

Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization pp. 12

Huang Hsin-Hsiung, Hao Shuai, Alarcon Saul and Yang Jie

Empirical Bayesian approach to testing multiple hypotheses with separate priors for left and right alternatives pp. 13

Bansal Naveen K., Maadooliat Mehdi and Schrodi Steven J.

On the relation between the true and sample correlations under Bayesian modelling of gene expression datasets pp. 14

Jacobovic Royi

Volume 17, issue 3, 2018

Non-parametric estimation of population size changes from the site frequency spectrum pp. 10

Waltoft Berit Lindum and Hobolth Asger

A statistical method for measuring activation of gene regulatory networks pp. 11

Esteves Gustavo H. and Reis Luiz F. L.

Bayesian inference of selection in the Wright-Fisher diffusion model pp. 14

Gory Jeffrey J., Herbei Radu and Kubatko Laura S.

Multi-locus data distinguishes between population growth and multiple merger coalescents pp. 21

Koskela Jere

Volume 17, issue 2, 2018

On “A mutual information estimator with exponentially decaying bias” by Zhang and Zheng pp. 6

Zhang Jialin and Chen Chen

Noise-robust assessment of SNP array based CNV calls through local noise estimation of log R ratios pp. 11

Cosemans Nele, Claes Peter, Brison Nathalie, Vermeesch Joris Robert and Peeters Hilde

Additive varying-coefficient model for nonlinear gene-environment interactions pp. 18

Wu Cen, Zhong Ping-Shou and Cui Yuehua

Volume 17, issue 1, 2018

Distance-correlation based gene set analysis in longitudinal studies pp. 11

Sun Jiehuan, Herazo-Maya Jose D., Huang Xiu, Kaminski Naftali and Zhao Hongyu

Tests for comparison of multiple endpoints with application to omics data pp. 13

Marozzi Marco

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting pp. 28

Dazard Jean-Eudes, Ishwaran Hemant, Mehlotra Rajeev, Weinberg Aaron and Zimmerman Peter

Volume 16, issue 5-6, 2017

Approximate maximum likelihood estimation for population genetic inference pp. 291-312

Bertl Johanna, Ewing Gregory, Kosiol Carolin and Futschik Andreas

A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type pp. 313-331

Lakhal-Chaieb Lajmi, Greenwood Celia M.T., Ouhourane Mohamed, Zhao Kaiqiong, Abdous Belkacem and Oualkacha Karim

Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes pp. 333-347

Kotoka Ekua and Orr Megan

A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory pp. 349-365

Nooney Colleen, Barber Stuart, Gusnanto Arief and Gilks Walter R.

Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation pp. 367-386

Szefer Elena, Lu Donghuan, Nathoo Farouk, Beg Mirza Faisal and Graham Jinko

Bayesian estimation of differential transcript usage from RNA-seq data pp. 387-405

Papastamoulis Panagiotis and Rattray Magnus

A Bayesian hierarchical model for identifying significant polygenic effects while controlling for confounding and repeated measures pp. 407-419

McMahan Christopher, Baurley James, Bridges William, Joyner Chase, Kacamarga Muhamad Fitra, Lund Robert, Pardamean Carissa and Pardamean Bens

Volume 16, issue 4, 2017

FC1000: normalized gene expression changes of systematically perturbed human cells pp. 217-242

Lönnstedt Ingrid M. and Nelander Sven

Bayesian comparison of protein structures using partial Procrustes distance pp. 243-257

Ejlali Nasim, Faghihi Mohammad Reza and Sadeghi Mehdi

Confidence intervals for heritability via Haseman-Elston regression pp. 259-273

Sofer Tamar

A statistical test for detecting parent-of-origin effects when parental information is missing pp. 275-289

Sacco Chiara, Viroli Cinzia and Falchi Mario

Volume 16, issue 3, 2017

Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study pp. 159-171

Zhang Haixiang, Zheng Yinan, Yoon Grace, Zhang Zhou, Gao Tao, Joyce Brian, Zhang Wei, Schwartz Joel, Vokonas Pantel, Colicino Elena, Baccarelli Andrea, Hou Lifang and Liu Lei

Mixture model-based association analysis with case-control data in genome wide association studies pp. 173-187

Ali Fadhaa and Zhang Jian

Genetic association test based on principal component analysis pp. 189-198

Chen Zhongxue, Han Shizhong and Wang Kai

Comparing the performance of linear and nonlinear principal components in the context of high-dimensional genomic data integration pp. 199-216

Islam Shofiqul, Anand Sonia, Hamid Jemila, Thabane Lehana and Beyene Joseph

Volume 16, issue 2, 2017

No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data pp. 83-93

Lun Aaron T. L. and Smyth Gordon K.

Missing value imputation for gene expression data by tailored nearest neighbors pp. 95-106

Faisal Shahla and Tutz Gerhard

Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects pp. 107-132

Pecanka Jakub and Goeman Jelle

A time warping approach to multiple sequence alignment pp. 133-144

Arribas-Gil Ana and Matias Catherine

A Bayesian semiparametric factor analysis model for subtype identification pp. 145-158

Sun Jiehuan, Warren Joshua L. and Zhao Hongyu

Volume 16, issue 1, 2017

Statistical models and computational algorithms for discovering relationships in microbiome data pp. 1-12

Shaikh Mateen R. and Beyene Joseph

Binary Markov Random Fields and interpretable mass spectra discrimination pp. 13-30

Kong Ao and Azencott Robert

Comparison and visualisation of agreement for paired lists of rankings pp. 31-45

Donald Margaret R. and Wilson Susan R.

Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset pp. 47-58

Su Pei-Fang, Mau Yu-Lin, Guo Yan, Li Chung-I, Liu Qi, Boice John D. and Shyr Yu

Generalized partial linear varying multi-index coefficient model for gene-environment interactions pp. 59-74

Liu Xu, Gao Bin and Cui Yuehua

Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis pp. 75-81

Bureau Alexandre and Croteau Jordie